The problem is probably that you have a MS/MS filtering DIA Isolation Scheme with prespecified windows, and none of the windows contain that number.
That is, you should go to:
Settings > Transition Settings > Full Scan
and change the MS/MS filtering Isolation Scheme to something else.

It sounds like you already checked the "Min m/z" and "Max m/z" settings at "Settings > Transition Settings > Instrument".
Those settings affect the m/z's which Skyline will allow for both precursor and product ions.

The Isolation Scheme only affects the allowable precursor m/z's.

-- Nick

Thanks for a very interesting example! I note a handful of issues with getting this into Skyline, which you may have already figured out:

1) The syntax for describing n-mers in adducts (which we adopted from https://fiehnlab.ucdavis.edu/staff/kind/metabolomics/ms-adduct-calculator/) is nM rather than Mn, so for example your line:
  Acetic Acid    C2H4O2    1    [M6-H6+Fe3+O]    537.88
should be
  Acetic Acid    C2H4O2    1    [6M-H6+Fe3+O]    537.88

2) There are a handful of places where atomic symbol and count are swapped in the adduct descriptions, e.g. K2 should be 2K

3) Skyline will only understand "[M+63Cu(I)]" if simplified to "[M+Cu]"

4) Skyline isn't currently set up to handle the Cu65 isotope, I'll have to add that. When that's available (the next Skyline Daily, probably) "[M+65Cu(I)]" will only be understood if simplified to "[M+Cu65]" or "[M+Cu']", as seen in the attached tidied-up version of your file. But for now, those two lines won't be understood by Skyline and you'll have to delete them for import.

Best Regards,

Brian Pratt

Hi Brian and Nick,

Thank you so much. The rectified transition list worked like a charm ! Now the pipeline is executed as expected.

But with that our worst fear is realized. We have commendable amount of PEG / PPG, Acetic acid and Nylon 66 polymer contamination !!

So I would like your expert opinion on two facts:

1. Should these samples be discarded straight away and not suitable for analysis ? Or is there a way to **remove** the contaminant spectra from the files, then take them for proteomic analysis ?

2. Do these contaminants' spectra **overlap** the actual protein spectra and lead to any false positive / negative ??

Regards
Sangram

Hi Sangram,

I'm glad I could help with your transition list. But these are questions I'm really not qualified to answer - hopefully someone else will chime in.

I would think, though, that any analysis tool would benefit from having the complete picture rather than any kind of cherry-picked data. I would just make sure that whoever is doing the analysis is aware of the contamination.

Best regards,

Brian Pratt